<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<!-- saved from url=(0022)http://internet.e-mail --><!-- saved from url=(0022)http://internet.e-mail -->




  <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type">




  <title>reference</title>
</head>




<body>





&nbsp;<img style="width: 100px; height: 88px;" alt="" src="sl_logo.jpg"> &nbsp; &nbsp; <img style="width: 150px; height: 54px;" alt="" src="siFi_header.gif"><br>


<br>


<table style="text-align: left; width: 403px; height: 144px;" border="1" cellpadding="2" cellspacing="2">



  <tbody>



    <tr>



      <td>Name</td>



      <td>si-Fi</td>



    </tr>



    <tr>



      <td>Version</td>



      <td>2.6.0-0001 Beta</td>



    </tr>



    <tr>



      <td>Authors</td>



      <td>Stefanie L&uuml;ck, Dimitar Douchkov</td>



    </tr>



    <tr>



      <td>Created</td>



      <td>2009-2011</td>



    </tr>



    <tr>



      <td>License</td>



      <td>GNU General Public License (GPL)</td>



    </tr>





  </tbody>
</table>


&nbsp;<br>


<h1>References</h1>


<ol>


  <li> Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient
alignment of short DNA sequences to the human genome. <i>Genome Biol</i> <span style="font-weight: bold;">10</span>:R25.</li>


  <li>Naito Y, Yamada T, Ui-Tei K, Morishita S, Saigo K (2004) siDirect: highly effective, target-specific
  siRNA design software for mammalian RNA interference.
  <i>Nucleic Acids Res.</i> <b>32</b>(Web Server issue):W124
  </li>


  <li>Ui-Tei K, Naito Y, Takahashi F, Haraguchi T, Ohki-Hamazaki H, Juni A, Ueda R, Saigo K (2004
  Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference.
  <i>Nucleic Acids Res.</i> <b>32:936</b>
  </li>


  <li>Naito Y, Yamada T, Matsumiya T, Ui-Tei K, Saigo K, Morishita
S (2005) dsCheck: highly sensitive off-target search software for
double-stranded RNA-mediated RNA interference. <i>Nucleic Acids Res.</i> <b>33</b>(Web Server issue):W589 .
  </li>


  <li>Gong W, Ren Y, Xu Q, Wang Y, Lin D, Zhou H, Li T (2006)
Integrated siRNA design based on surveying of features associated with
high RNAi effectiveness. <i>BMC Bioinformatics</i> <b>7</b>:516
  </li>


  <li>Pei Y, Tuschl T (2006) On the art of identifying effective and specific siRNAs. <i>Nat. Methods</i> <b>3(9)</b>:670
  </li>


  <li>Xu P, Zhang Y, Kang L, Roossinck MJ, Mysore KS (2006) Computational Estimation and Experimental Verification of
Off-Target Silencing during Posttranscriptional Gene Silencing in Plants. <i>Plant Physiol.</i> <b>142(2)</b>:429
  </li>


</ol>



<h1>Software libraries</h1>



Python 2.7<br>



<br>



<a href="http://www.python.org"><img title="Python" style="border: 2px solid ; width: 214px; height: 70px;" alt="Python" src="python.png"></a><br>



<br>



wxPython 2.8.11.0<br>



<a href="Python"><img style="border: 2px solid ; width: 214px; height: 135px;" alt="wxPython" title="wxPython" src="splash.png"></a><br>



<br>



Biopython 1.57<br>



<br>



<a href="http://www.biopython.org"><img style="border: 2px solid ; width: 150px; height: 94px;" alt="Biopython" src="biopython_small.jpg_bigger.jpeg"></a><br>



<br>
Bowtie 0.11.3<br>
<a href="http://bowtie-bio.sourceforge.net/index.shtml">http://bowtie-bio.sourceforge.net/index.shtml</a>
</body>
</html>
